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Dear Florian,
 
Could it be that you only have spots in the center of your image and that XDS is trying to process a lot of image area with only background in it? In this case it will try to build profiles from non-existing reflections and start to complain. The resulting bad data may cause scala to crash.
Look in the XDS.INP file for an INCLUDE_RESOLUTION_RANGE keyword and set it to some sensible value with a high resolution cut-off of say 5 or 6 Å. This should solve your problem.
 
Best,
HErman

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Florian Schmitzberger
Sent: Thursday, March 08, 2012 3:49 PM
To: [log in to unmask]
Subject: [ccp4bb] xds - problem with reference profile

Dear All,

I am getting a warning message in XDS I have not seen before, when trying to integrate a low resolution (~ 7 A) dataset. 

!!! WARNING !!! REFERENCE PROFILE #  1 IS EMPTY.
                 THE AVERAGE PROFILE IN THIS BATCH IS USED INSTEAD.

and so forth for the other reference profiles. 

Indexing works alright with XDS; with likely point group C2. Scaling the data integrated with XDS, with Scala fails; apparently most of the reflections are rejected. 

What are probable causes for the above error message?

Cheers,

Florian